Various environmental changes were associated with the Permian-Triassic mass extinction at 252.2 Ma. Diverse unusual sediments and depositional phenomena have been uncovered as responses to environmental and biotic changes. Lithological and detailed conodont biostratigraphic correlations within six Permian-Triassic boundary sections in South China indicate rapid fluctuations in carbonate deposition. Four distinct depositional phases can be recognized:(1) normal carbonate deposition on the platform and slope during the latest Permian;(2) reduced carbonate deposition at the onset of the main extinction horizon;(3) expanded areas of carbonate deposition during the Hindeodus changxingsensis Zone to the H. parvus Zone; and(4) persistent mud-enriched carbonate deposition in the aftermath of the Permian-Triassic transition. Although availability of skeletal carbonate was significantly reduced during the mass extinction, the increase in carbonate deposition did not behave the same way. The rapid carbonate depositional changes, presented in this study, suggest that diverse environmental changes played key roles in the carbonate deposition of the Permian-Triassic mass extinction and onset of its aftermath. An overview of hypotheses to explain these changes implies enhanced terrestrial input, abnormal ocean circulation and various geobiological processes contributed to carbonate saturation fluctuations, as the sedimentary response to large volcanic eruptions.